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Tackle Jonas Jennings had surgery this morning, for the third time, on his frozen right shoulder and will be placed on season-ending injured reserve. Jennings played two games this year before his shoulder popped out of joint in the third game against Detroit and was listed an emergency third tackle for the last two games but didn’t see any action.

This time the surgery, which is designed to tighten the shoulder, will require a six-month recovery. General manager Scot McCloughan said he wasn’t sure Jennings would remain with the team next season.

“It’s something we’re going to address at the end of the season. But as of right now he’s a 49er,” McCloughan said. “It’s not his fault that he got hurt. It’s not his fault that the record is the way it is. I think he’s done everything in his power to try and get back and try to be able to play for us. As you guys are well aware, when he did play for us he has played well.”

In a way, Jennings has symbolized the 49ers’ plight for the last four seasons. He was former coach Mike Nolan’s first acquisition, signing a six-year $36 million deal shortly after Nolan was hired in January of 2005. Jennings came into his introductory news conference and immediately connected with the media with his natural bonhomie. At that setting, he said he was “Rollin’ with Nolan.”

But because of injuries, Jennings didn’t roll enough and the warm feeling he engendered that day quickly soured along with the team’s fortunes for the next four years.

Much like what occurred this year, Jennings started off well as the team’s left tackle in 2005 and then threw out his right shoulder for the first time and missed the rest of the season. He returned in 2006, and played his best season. The 49ers’ became a decidedly left-handed running team behind Jennings and left guard Larry Allen. The team won seven games, Frank Gore ran for a franchise record 1,695 yards and the popular Jennings was voted as a permanent team captain by his teammates along with quarterback Alex Smith, defensive tackle Bryant Young, cornerback Walt Harris and safety Keith Lewis.

Last season, a personal matter and an ankle injury requiring surgery held him to five games before he was again placed on injured reserve. Throughout his injury ordeals, his toughness was questioned by teammates and coaches, some of whom felt Jennings quit on them. He also quarreled with former line coach George Warhop at times last year. Warhop was fired along with head coach Mike Nolan on the week of Oct. 26.

The team signed 6-7, 320-pound Jacob Bender off the Jets’ practice squad to take Jennings’s spot on the roster and back up the tackle spots. McCloughan said Jennings could have stayed on the rest of the year as an emergency backup, but McCloughan liked the way Adam Snyder has played the at right tackle the last two games and he expects Barry Sims to return from the ankle sprain that’s sidelined him the last two games this week, which cleared the way to place Jennings on I.R. for the third time in four seasons.